1. LifeWatch - ICT infrastructure for Biodiversity Research in Europe LifeWatch ICT construction group (WP5) Axel Poigné, Vera Hernández ( Fraunhofer IAIS) Alex Hardesty (Cardiff University)

2. Contents Biodiversity Research. What is it about ? An Example: Pollination What is Lifewatch LifeWatch ICT Infrastructure shall be … Challenges (and Solutions)

3. LifeWatch on a Slide What lives Where & when Why (together) For how long

4. An Example: Pollination Factors Pollinators Climate / Soil Vegetation / Horticulture Evolution Pollination management Decline due to ? Fertilisation / Pesticides Diseases / Parasitism Habitat destruction Monoculture

5. What is LifeWatch? An e-Science infrastructure –Exploration of patterns of biodiversity and processes of biodiversity across time and space –What causes species diversity? A European Research Infrastructure –Distributed observatories / sensors –Databases, processing and analytical tools –Computational capability and capacity –Collaborative environments –Support, training, partnering, fellowship Open access, single portal

6. 200820092010 initial decision final decision logistics construction Earlier projectsConceptionPreparationsConstruction Operation & Evolution 1995 2005200820112016 Construction ‘blue print’ Political commitment €5m~ €375m Status: The LifeWatch timeline

7. The LifeWatch ICT Infrastructure shall be… a distributed system of nodes Core ICT Components National Components / Services LifeWatch ICT Infrastructure

8. The LifeWatch ICT Infrastructure shall be… an interoperable access (and publishing) mechanism of data and services from a variety of sources Core ICT Components National Components / Services STANDARDSSTANDARDS LifeWatch ICT Infrastructure Other providers

9. The LifeWatch ICT Infrastructure shall be… a mean of processing and scaling-up biodiversity data Scale Ecosystems Species DNA, proteins and genes Time and evolution Phylogenomics & Biogeography Taxonomy & Systematics Species Richness & Ecosystem Services Biodiversity Valuation Species Distribution Dynamics Genes-Species-Specimens (multi-scale linkages) Citizen Science & Observations Data transformation Data processing Workflows

10. (*) De Roure & Goble, "Software Design for Empowering Scientists," IEEE Software, vol. 26, 2009 The LifeWatch ICT Infrastructure shall be… Discovery Acquisition Preparation/Cleaning Transformation/Fusion Interpretation Dissemination Curation Provenance Identity & Naming Security/Access Lifecyle a support for the full eLab lifecycle

11. The LifeWatch ICT Infrastructure shall be… a collaborative environment (*) AdHoc Software (http://www.gridwisetech.com) (*)

12. 5 challenges (and 5+ solutions) HETEROGENEITY of the community’s requirements, its data resources and tools GAP between current practice and future vision SCALE of implementation of a pan-European infrastructure, €375m, >25,000 users PACE of innovation in ICTs FIT with mainstream industry and Higher Education / Research sector directions for ICT service

13. Challenge of HETEROGENEITY: Interconnected nature of biodiversity ideas, outputs, repositories From Peterson et al (2010), Syst Biodivers 8(2), 159-168 From Guralnick and Hill (2010), http://www.slideshare.net/robgur/ievobio-keynote-talk-2010http://www.slideshare.net/robgur/ievobio-keynote-talk-2010

14. Solution for HETEROGENEITY : SOA approach Tools Names Dictio- naries Onto- logies Data providers Data providers Mediation services Data access services Annotation services Identification services Discovery services Information management services User manage- ment services Human interaction services Portrayal services Interaction services Personalization services Collaboration services Communica- tion services Encoding services Transformation Services Messaging services Transfer services Services Files Metadata services Spatial pro- cessing services Analytical & Modelling services Taxonomic pro- cessing services integration services Processing services Orchestration services Workflow services Source Integration services Integration services System management services Monitoring services Service mana- gement services Transaction services Quality evaluation services Security services (AAA) Provenance services Applications Portals E-labsRich web applications Visualisation services Sensors Thematic data access services Thematic interaction services Thematic pro- cessing services Service Bus

15. Genome annotations Genome annotations GO Model organisms Model organisms NCBI Taxonomy Genetic knowledge bases OMIM Other subdomains Other subdomains … Anatomy FMA UMLS Addison Disease (id:D000224) Addison's disease (id:363732003) Biomedical literature Biomedical literature MeSH Clinical repositories Clinical repositories SNOMED CT UMLS C0001403 Solution for HETEROGENEITY : Semantic interoperability through knowledge management Unified Medical Language System (UMLS) from: Olivier Bodenreider, Lister Hill National Center for Biomedical Comunications, Bethesda, Maryland, USA

16. Heart Concepts Metathesaurus 38 237 49 5 16 1322 Esophagus Left Phrenic Nerve Heart Valves Fetal Heart Medias- tinum Saccular Viscus Angina Pectoris Cardiotonic Agents Tissue Donors Anatomical Structure Fully Formed Anatomical Structure Embryonic Structure Body Part, Organ or Organ Component Pharmacologic Substance Disease or Syndrome Population Group Semantic Types Semantic Network Unified Medical Language System (UMLS) from: Olivier Bodenreider, Lister Hill National Center for Biomedical Comunications, Bethesda, Maryland, USA

17. 5 challenges (and 5+ solutions) HETEROGENEITY of the community’s requirements, its data resources and tools GAP between current practice and future vision SCALE of implementation of a pan-European infrastructure, €386m, >25,000 users PACE of innovation in ICTs FIT with mainstream industry and Higher Education / Research sector directions for ICT service

18. GAP: Between current practice and future vision “collaborative, distributed research methods that exploit advanced computational thinking” Malcolm Atkinson, 2007

19. GAP solution: Workflow paradigm BioDivCapability..… Workflow Service BioDivCapability..… used in delivers used in

20. 5 challenges (and 5+ solutions) HETEROGENEITY of the community’s requirements, its data resources and tools GAP between current practice and future vision SCALE of implementation of a pan-European infrastructure, €386m, >25,000 users PACE of innovation in ICTs FIT with mainstream industry and Higher Education / Research sector directions for ICT service

21. Challenge of PACE: Of innovation in ICT New technologies, products, services, possibilities, every day –Seeing the wood for the trees Technology decisions –2 years ago for construction that starts now –that have to last for 10 years?

22. PACE solution: Divorce functionalities from technologies LifeWatch Reference Model –Basis of technical strategy Standards-based –ORCHESTRA RM –OGC RM –INSPIRE Viewpoints –Enterprise, Information, Service –Engineering, Technology

23. The LifeWatch Reference Model (“LifeWatch-RM”) Gives 3 freedoms: Technology independence Ability to extend technical capabilities –Functionalities expressed as services –Applications as networks of service instances Support for thematic extensions FQI Abstract Service Platform Concrete Service Platform Service Network Requirements I: Information F: Functionality Q: Quality of service/non functional Problem abstract design concrete design engineering LifeWatch Reference Model W3C Web Services Operation Policies rules

24. Components: e.g. Information Model Schema Feature Application Schema (AS) Application Schema for Meta-Information Feature Set Meta-Info Base is associated with describes features according to purpose extracted from converted from structure defined by Source System Semantic Domain Ontologies Levels Meta- model "Meta-model aspect" “Semantic aspect" Meta Model used for “Information aspect" "Meta-information aspect" Purposes influenced by rules defined by Semantics derived from

25. Further elements Service model Service network Engineering policies Implementation rules Meta model

26. Why a Reference Model … LifeWatch ICT Infrastructure LifeWatch Developer Data, Services Data Provider

27. Why a Reference Model … Data Catalogue Annotation Repository Citation Prove- nance Rep. Service Catalogue Applica- tion Server Enterprise Service Bus Authenti- Cation Authori- sation User Manage- ment Catalogue Feature Access Name Service Monitoring Map & Diagram Thesaurus Access Ontology Access Format Conver- sion Gazetteer Service Chaining Workflow Enactment Notificatio n Processin g Annotation Semantic Annotation Sensor Access Modelling Taxonomy Access Species occurrenc e Species Distributio n Geocoder Data Interpola- tion View & Explore Curation Data Publishing Browse & Search Web Content Manage- ment Provenanc e Login & Profile Workflow Editing Communic ation User annotation Data Manage- ment Communit y Support Virtual Laborato- ries

28. A The Goal Portal Virtual Collaborative environments AA Security Access to external Services ProvenanceProvenance Catalogue(s) Annotations Services Semantic Mediation PublicationPublication Computational Resources Workflows